I'm not using the eclipse plugin for linux. I set my dev environment in the following way:
1) create a directory with the whole JDE (install it on a windows box and copy it across on linux)
2) Install the Sun WTK (you will need it to run preverify)
3) in your ant script import bb-ant (which you would havepreviously downloaded) and have the correct targets
<property name="jde.home" value="${user.home}/dev/bbjde" />
<property name="output.basename" value="MyApplication" />
<property name="src" value="../src" />
<taskdef resource="bb-ant-defs.xml" />
<target name="build">
<mkdir dir="${build.dir}" />
<rapc output="${output.basename}" srcdir="${src}" destdir="${build.dir}" quiet="false">
<jdp title="My Blackberry Client" vendor="MySelf" version="1.1.4" type="cldc" runonstartup="true" startuptier="7" icon="../resources/icon.png" />
</rapc>
</target>
<target name="sign" depends="build">
<sigtool codfile="${build.dir}/${output.basename}.cod" password="znetworks"/>
<delete file="LogFile.txt" />
</target>
4) Make sure that the bb-ant is in your ant classpath
5) Make sure that, when you run eclipse, you have the bin directory of WTK and the JDE in your path
6) Just build from the ant task
Unfortunately I couldn't get the simulator running on Linux yet, so I just mount the build directory in a directory on a windows virtual box and run it from there
Hope this helps,
Oliver